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BamToBfq (Picard)

Converts a BAM file into a BFQ (binary fastq formatted) file.

The BFQ format is the input format to some tools like Maq aligner.

Input

A single BAM file to convert

Output

One or two FASTQ files depending on whether the BAM file contains single- or paired-end sequencing data. You must indicate the output directory that will contain these files (ANALYSIS_DIR) and the output file name prefix (OUTPUT_FILE_PREFIX).

Usage example:

java -jar picard.jar BamToBfq \
     I=input.bam \
     ANALYSIS_DIR=output_dir \
     OUTPUT_FILE_PREFIX=output_name \
     PAIRED_RUN=false

Category Read Data Manipulation


Overview

Converts a BAM file into a BFQ (binary fastq formatted) file.

The BFQ format is the input format to some tools like Maq aligner.

Input

A single BAM file to convert

.

Output

One or two FASTQ files depending on whether the BAM file contains single- or paired-end sequencing data. You must indicate the output directory that will contain these files (ANALYSIS_DIR) and the output file name prefix (OUTPUT_FILE_PREFIX).

Usage example:

     java -jar picard.jar BamToBfq \
             I=input.bam \
             ANALYSIS_DIR=output_dir \
             OUTPUT_FILE_PREFIX=output_name \
             PAIRED_RUN=false
 

BamToBfq (Picard) specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Required Arguments
--ANALYSIS_DIR
null The analysis directory for the binary output file.
--FLOWCELL_BARCODE
 -F
null Flowcell barcode (e.g. 30PYMAAXX).
--INPUT
 -I
null The BAM file to parse.
--OUTPUT_FILE_PREFIX
null Prefix for all output files
--PAIRED_RUN
 -PE
null Whether this is a paired-end run.
Optional Tool Arguments
--arguments_file
[] read one or more arguments files and add them to the command line
--BASES_TO_WRITE
null The number of bases from each read to write to the bfq file. If this is non-null, then only the first BASES_TO_WRITE bases from each read will be written.
--CLIP_ADAPTERS
true Whether to clip adapters from the reads
--help
 -h
false display the help message
--INCLUDE_NON_PF_READS
 -NONPF
false Whether to include non-PF reads
--LANE
 -L
null Lane number.
--READ_CHUNK_SIZE
 -CHUNK
2000000 Number of reads to break into individual groups for alignment
--READ_NAME_PREFIX
null Prefix to be stripped off the beginning of all read names (to make them short enough to run in Maq)
--READS_TO_ALIGN
 -NUM
null Number of reads to align (null = all).
--RUN_BARCODE
 -RB
null Deprecated option; use READ_NAME_PREFIX instead
--version
false display the version number for this tool
Optional Common Arguments
--COMPRESSION_LEVEL
5 Compression level for all compressed files created (e.g. BAM and VCF).
--CREATE_INDEX
false Whether to create a BAM index when writing a coordinate-sorted BAM file.
--CREATE_MD5_FILE
false Whether to create an MD5 digest for any BAM or FASTQ files created.
--GA4GH_CLIENT_SECRETS
client_secrets.json Google Genomics API client_secrets.json file path.
--MAX_RECORDS_IN_RAM
500000 When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
--QUIET
false Whether to suppress job-summary info on System.err.
--REFERENCE_SEQUENCE
 -R
null Reference sequence file.
--TMP_DIR
[] One or more directories with space available to be used by this program for temporary storage of working files
--USE_JDK_DEFLATER
 -use_jdk_deflater
false Use the JDK Deflater instead of the Intel Deflater for writing compressed output
--USE_JDK_INFLATER
 -use_jdk_inflater
false Use the JDK Inflater instead of the Intel Inflater for reading compressed input
--VALIDATION_STRINGENCY
STRICT Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
--VERBOSITY
INFO Control verbosity of logging.
Advanced Arguments
--showHidden
false display hidden arguments

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.


--ANALYSIS_DIR / NA

The analysis directory for the binary output file.

R File  null


--arguments_file / NA

read one or more arguments files and add them to the command line

List[File]  []


--BASES_TO_WRITE / NA

The number of bases from each read to write to the bfq file. If this is non-null, then only the first BASES_TO_WRITE bases from each read will be written.

Integer  null


--CLIP_ADAPTERS / NA

Whether to clip adapters from the reads

boolean  true


--COMPRESSION_LEVEL / NA

Compression level for all compressed files created (e.g. BAM and VCF).

int  5  [ [ -∞  ∞ ] ]


--CREATE_INDEX / NA

Whether to create a BAM index when writing a coordinate-sorted BAM file.

Boolean  false


--CREATE_MD5_FILE / NA

Whether to create an MD5 digest for any BAM or FASTQ files created.

boolean  false


--FLOWCELL_BARCODE / -F

Flowcell barcode (e.g. 30PYMAAXX).

Exclusion: This argument cannot be used at the same time as OUTPUT_FILE_PREFIX.

R String  null


--GA4GH_CLIENT_SECRETS / NA

Google Genomics API client_secrets.json file path.

String  client_secrets.json


--help / -h

display the help message

boolean  false


--INCLUDE_NON_PF_READS / -NONPF

Whether to include non-PF reads

Boolean  false


--INPUT / -I

The BAM file to parse.

R File  null


--LANE / -L

Lane number.

Exclusion: This argument cannot be used at the same time as OUTPUT_FILE_PREFIX.

Integer  null


--MAX_RECORDS_IN_RAM / NA

When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.

Integer  500000  [ [ -∞  ∞ ] ]


--OUTPUT_FILE_PREFIX / NA

Prefix for all output files

Exclusion: This argument cannot be used at the same time as FLOWCELL_BARCODE, LANE.

R String  null


--PAIRED_RUN / -PE

Whether this is a paired-end run.

R Boolean  null


--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean  false


--READ_CHUNK_SIZE / -CHUNK

Number of reads to break into individual groups for alignment

Integer  2000000  [ [ -∞  ∞ ] ]


--READ_NAME_PREFIX / NA

Prefix to be stripped off the beginning of all read names (to make them short enough to run in Maq)

String  null


--READS_TO_ALIGN / -NUM

Number of reads to align (null = all).

Integer  null


--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null


--RUN_BARCODE / -RB

Deprecated option; use READ_NAME_PREFIX instead

Exclusion: This argument cannot be used at the same time as READ_NAME_PREFIX.

String  null


--showHidden / -showHidden

display hidden arguments

boolean  false


--TMP_DIR / NA

One or more directories with space available to be used by this program for temporary storage of working files

List[File]  []


--USE_JDK_DEFLATER / -use_jdk_deflater

Use the JDK Deflater instead of the Intel Deflater for writing compressed output

Boolean  false


--USE_JDK_INFLATER / -use_jdk_inflater

Use the JDK Inflater instead of the Intel Inflater for reading compressed input

Boolean  false


--VALIDATION_STRINGENCY / NA

Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.

The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:

STRICT
LENIENT
SILENT

ValidationStringency  STRICT


--VERBOSITY / NA

Control verbosity of logging.

The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:

ERROR
WARNING
INFO
DEBUG

LogLevel  INFO


--version / NA

display the version number for this tool

boolean  false


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GATK version 4.1.0.0 built at Wed, 30 Jan 2019 10:21:04 +0530.